The aim of the study is to compare the performance of Cobas Amplicor HCV RNA v2.0 (Roche Diagnostics, ABD) with Real Art HCV RG RT PCR (Artus GmbH, Germany) in quantitation of HCV RNA. 70 serum samples of patients with chronic hepatitis C that were admitted to the laboratory for HCV RNA quantitation were included in the study. Samples were tested by two different methods and the results were compared. To assess the reproducibility of the test, 6 serum samples were tested in different runs and another six samples in the same run in duplicate. 1/10, 1/100,1/1000 and 1/10000 dilutions of serum samples were also quantitated. Twenty-one samples with Cobas Amplicor and 35 samples with rotorgene were below the level of 500.000 IU/ml. Spearmen correlation test showed no correlation between the two assays when negative samples were excluded (correlation coefficient= 0.309). The logarithmic difference between the Cobas Amplicor System and HBV Monitor Realart HCV PCR test ranged between 0.1 and 1.3 (median 0.7, mean 0.7). For the same samples tested in different runs and in the same run logarithmic differences were 0.04,0.3 and 0.01,0.07 respectively. Difference between these results was not significant by Wilcoxon test (z=0.178, p=0.859). In diluted samples regresion in viral load was linear. RealArt HCV RG RT PCR is a reproducible assay with a wide dynamic range of HCV RNA quantitation. Because of the lack of correlation between two assays it is not appropriate to convert the test results of different methods for follow up a patient.